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problem encounterd when I used cg_bonds.tcl
- Jinyoung
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2 years 8 months ago - 2 years 8 months ago #9108
by Jinyoung
problem encounterd when I used cg_bonds.tcl was created by Jinyoung
Hi,
I tried to visualize the MARTINI force field system with VMD by using cg_bonds.tcl
When I used cg_bonds.tcl,
But before I prompt VMD, I source gromacs as below:
how can I solve this problem?
Best regards
Jinyoung
I tried to visualize the MARTINI force field system with VMD by using cg_bonds.tcl
When I used cg_bonds.tcl,
vmd > cg_bonds -top system.top
key "na" not known in dictionary
vmd > cg_bonds -tpr ../PROD/prod_1.tpr
couldn't execute "/usr/bin/gmxdump": no such file or directory
But before I prompt VMD, I source gromacs as below:
source ~/apps/GROMACS/gromacs-2020.4_gcc-7.5.0_openmpi-4.0.2/bin/GMXRC
how can I solve this problem?
Best regards
Jinyoung
Last edit: 2 years 8 months ago by Jinyoung.
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- riccardo
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2 years 8 months ago #9112
by riccardo
Replied by riccardo on topic problem encounterd when I used cg_bonds.tcl
This is a problem pf cg_bonds with newer Gromacs version. cg_bonds is looking for "gmxdump" which was renamed in recent Gromacs version.
Try using the following:
*NOTE* that your path to "gmx" might be different! Look for where Gromacs is installed and where that "gmx" file is.
Try using the following:
cg_bonds [b]-gmx /usr/local/gromacs/bin/gmx[/b] -tpr ...
*NOTE* that your path to "gmx" might be different! Look for where Gromacs is installed and where that "gmx" file is.
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- Jinyoung
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2 years 7 months ago #9156
by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below
child process exited abnormally
The error message is below
child process exited abnormally
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- Jinyoung
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2 years 7 months ago #9157
by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below
child process exited abnormally
The error message is below
child process exited abnormally
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- Jinyoung
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2 years 7 months ago #9158
by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below
child process exited abnormally
The error message is below
child process exited abnormally
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- Jinyoung
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2 years 7 months ago #9166
by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below
child process exited abnormally
The error message is below
child process exited abnormally
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- riccardo
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2 years 4 months ago #9254
by riccardo
Replied by riccardo on topic problem encounterd when I used cg_bonds.tcl
It would be useful if you specified the command you used.
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